Import and local transmission analysis
The input for this analysis is the results from the maximum likelihood mapping of the geographical states on the full phylogenetic tree of the 9732 genomes.
Import versus local transmission for Norway, Australia, Europe and the USA
From the mapped geographical lineage distributions we can derive the number of importation and local transmission events for each location (based on the available sequences). NB. we do not account for unobserved infections (sequences), and hence the estimated number only reflects the fraction of sequenced genomes that is assigned to specific lineages. The relative growth between the lineages (growth of an transmission lineage implies local transmission), is an important quantity and tells us how dominant specific lineages have become over time. This too could be affected by nonrandom sampling such as targeted sampling of lineages with anitibiotic resistance.
Cumulative growth of transmission lineages
The following plots show the cumulative number of sequences obtained from each estimated transmission lineage over time
name_date_NOR = name_date[name_date$name%in%nor_tips,]
linfo_NOR = lineage_info(Result_NOR,name_date = name_date_NOR)
LineageHomology::lineage_growth_cumulative(linfo_NOR,datelims=c("2015-01-01","2019-06-15","1 year"))
name_date_AUS = name_date[name_date$name%in%aus_tips,]
linfo_AUS = lineage_info(Result_AUS,name_date = name_date_AUS)
LineageHomology::lineage_growth_cumulative(linfo_AUS,datelims=c("2016-07-01","2018-06-15","5 months"))
name_date_USA = name_date[name_date$name%in%usa_tips,]
linfo_USA = lineage_info(Result_USA,name_date = name_date_USA)
LineageHomology::lineage_growth_cumulative(linfo_USA,datelims=c("2008-07-01","2019-06-15","2 year"))
name_date_EUR = name_date[name_date$name%in%eur_tips,]
linfo_EUR = lineage_info(Result_EUR,name_date = name_date_EUR)
LineageHomology::lineage_growth_cumulative(linfo_EUR,datelims=c("2008-07-01","2019-06-15","2 year"))
Aggregated estimates of import, local transmission and export over the full phylogeny:
c1 = Summarize_import_export_local_transmission(implocexp_NOR); c1## 2.5% 50%
## Import 706.850000 736.0000000
## Local transmission 1929.425000 1967.5000000
## Export 922.475000 980.5000000
## Import / ( Import + Local transmission - export) 0.412446 0.4271619
## 97.5%
## Import 764.0000000
## Local transmission 2004.0500000
## Export 1028.0000000
## Import / ( Import + Local transmission - export) 0.4390678c2 = Summarize_import_export_local_transmission(implocexp_AUS); c2## 2.5% 50%
## Import 356.4750000 371.5000000
## Local transmission 2152.0000000 2175.0000000
## Export 312.4750000 346.0000000
## Import / ( Import + Local transmission - export) 0.1623292 0.1688253
## 97.5%
## Import 391.0000000
## Local transmission 2199.0500000
## Export 381.6750000
## Import / ( Import + Local transmission - export) 0.1770533c3 = Summarize_import_export_local_transmission(implocexp_USA); c3## 2.5% 50%
## Import 370.9500000 390.0000000
## Local transmission 2574.3750000 2595.5000000
## Export 586.9000000 617.0000000
## Import / ( Import + Local transmission - export) 0.1572872 0.1646612
## 97.5%
## Import 407.5750000
## Local transmission 2620.1000000
## Export 645.0000000
## Import / ( Import + Local transmission - export) 0.1710577c3 = Summarize_import_export_local_transmission(implocexp_EUR); c3## 2.5% 50%
## Import 449.4750000 476.0000000
## Local transmission 4233.9500000 4266.5000000
## Export 620.0000000 643.5000000
## Import / ( Import + Local transmission - export) 0.1106148 0.1161259
## 97.5%
## Import 499.5250000
## Local transmission 4306.0000000
## Export 662.0000000
## Import / ( Import + Local transmission - export) 0.1205556In Norway we estimate that around 27% of locally observed cases can
be attributed due to importation events.
This is more than twice that estimated for the other locations
(Australia, the USA, and Europe in general).
Stratifying the estimates on the periods 2010-2014, 2014-2018, and 2010-2018 (total), we obtain the following estimates
By dividing importation and exportation by (import + local transmission) and (export + local transmission), respectively, we obtain the following estimates:
The fraction of total events that are imports, exports and local transmissions in the period 2000-2018 are visualized below.
#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_NOR.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_NOR)
#dev.off()
#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_AUS.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_AUS)
#dev.off()
#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_USA.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_USA)
#dev.off()
#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_EUR.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_EUR)
#dev.off()The absolute estimates on the same periods are shown below.
